On 12/3/17 8:01 AM, rose rahmani wrote:
On Tue, Nov 28, 2017 at 5:11 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 11/28/17 12:23 AM, rose rahmani wrote:
Hello;
I took 2000 configuration from trajconv. Amino acid is in its normal shape
till almost conf1000.gro(and a little more). But in for example
conf1300.gro amino acid was disintegrated. What does it mean? Would you
please help me?
Bonds can't break and molecules can't "disintegrate" - what you're seeing
is probably a result of PBC.
http://www.gromacs.org/Documentation/Terminology/Periodic_
Boundary_Conditions
I don't know why this doesn't work since yesterday?!!!!...anyway...
I used trjconv for just one frame for example conf2000;
trjconv -f conf2000.gro -n index.ndx -s pull.tpr -o new_conf2000.gro -pbc
whole
so protein turned into to its normal shape, but i'm not sure does it makes
sense or not?! is that right? if it's right, another problem is;
protein is getting out of box, should i use trjconv for centering?
Thank you for your attentions
A "whole" molecule only matters for visualization. It has no impact on
physical interactions computed by mdrun.
-Justin
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
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